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Polluted water is heading for the Great Barrier Reef in the wake of Cyclone Debbie, Queensland scientists say.

Griffith University associate professor Andrew Brooks has released photographs he took during an aerial survey of the area after the category five cyclone coasts.

Dr Brooks said much of the deluge fell in a well-known erosion hot spot in the Burdekin catchment in Queensland's north.

He said the 11,000-square-kilometre area generates 30 per cent of all sediment that flows to the reef.

"Erosion from this hot spot must be significantly reduced to protect the reef," Dr Brooks said.

"We know sediment can harm coral and sea grass by restricting light. Now we're learning that sediment from this area also carries large loads of harmful nitrogen because it sticks to the sediment sourced from these same soils."

Dr Brooks said the state and federal governments were taking the erosion issue seriously, as evident through their investment in the area.

"I'm hoping that commitment continues with the level of funding required to rehabilitate the area," he said.

Pictures also show the flood plumes from the Burdekin and Fitzroy rivers heading into the ocean.

The World Wildlife Fund said it was concerned by the pictures because the Great Barrier Reef had suffered "unprecedented" coral bleaching events for the past two years.

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